"We agreed on a parallel probe into the reasons why it took so long to implement this project. And we have reached not very pleasant conclusions," Sergei Stepashin told the state-owned Rossia television channel.
Russia is helping Iran build the Bushehr nuclear power plant, over the strenuous objections of the United States and Israel.
Tehran wants to question former Russian nuclear energy minister Yevgeny Adamov, arrested in Switzerland two months ago, about his alleged involvement in embezzlement linked to the work at Bushehr, said Stepashin, who recently visited Iran.
"The Iranians have many questions for former minister Adamov, because, according to their data, several projects worth a lot of money, millions of dollars, were paid for but have not been implemented," Stepashin said.
Adamov, who was a minister from 1998 to 2001, was arrested in Switzerland last May at the request of the United States and is still being held there. Moscow has requested his extradition to Russia to answer charges of embezzlement.
The US justice department accuses him and an accomplice of having misappropriated, between 1993 and 2003, nine million dollars the United States paid Russia to improve security in its nuclear facilities.
Stepashin particularly criticized the part played the AtomStroiExport company, which he said had been set up in 1998 under the authority of the Russian nuclear energy ministry and was acting as an intermediary for Russia's nuclear programs in Iran.
"We are waiting for our Iranian colleagues (to send us) documents and we will study them very closely with our specialists," Stepashin said, adding that the Russian general prosecutor's office might also take an interest in them.
Both the United States and Israel have objected to the building of the Bushehr reactor, which could go online at the end of next year, as they claim Iran is secretly trying to develop nuclear weapons and that having such a facility will be a proliferation risk.
Bushehr, which will be Iran's first nuclear power reactor, is being built under an agreement between the Russian and Iranian governments for 800 million dollars.
Russia signed a technological cooperation agreement with Tehran in 2002 that opened the way for the construction of up to five reactors -- including a second one at Bushehr -- over the coming 10 years.